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    <title>Data analysis - Student's t-test and Fold Change</title>
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<h1>One-way ANOVA test</h1>

<h2>Description</h2>
<p>
    This module performs One-way analysis of variance (abbreviated ANOVA) test on the intensities
    of aligned features and calculates the corresponding p-values.
</p>
<p>
    The ANOVA technique is used to compare mean intensities of two or more groups of raw data files.
    The groups of raw data files are specified by a user. Then ANOVA tests the null hypothesis that
    the intensities of aligned features have the same mean values in all groups. The ANOVA produces
    an F-statistic and the corresponding p-value. If p-value is close to zero (typically less than
    0.05), then the intensities of aligned features are significantly different in two or more
    groups.
</p>

<h2>Example</h2>
<ol>
    <li>
        <b>Set a group parameter for each raw data file.</b> Choose menu "Project -> Set sample
        parameters". In the window <em>Setup project parameters and values</em>, click button
        "Add new parameter". In the window <em>Define new project parameter</em>, give a name to
        the parameter and add its values. Finally, in the window <em>Setup project parameters
        and values</em>, assign a value to each raw data file.

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            <p>
                <img src="user_parameter.png" alt="User parameters"/>
            </p>
        </div>
    </li>
    <li>
        <b>Perform One-way ANOVA test.</b> In the right pane of the main window, select an aligned
        peak list and choose menu "Peak list methods -> Data analysis -> One-way ANOVA test."
        In the field <em>Sample parameter</em>, select the name of the parameter that you specified
        in the previous step, and click button OK.

        <div align="center">
            <p>
              <img src="anova_test.png" alt="ANOVA test"/>
            </p>
        </div>
    </li>
    <li>
        <b>Export results.</b> In the right pane of the main window, select an aligned peak list
        and choose menu "Peak list methods -> Export/Import -> Export to CSV file." In the
        parameters window, check the option "Export quantitation results and other information."
        The exported CSV file will contain column <em>ANOVA_P_VALUE</em> with the p-values
        produced by the one-way ANOVA test.

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            <p>
                <img src="export.png" alt="CSV Export"/><br/>
                <img src="csv_file.png" alt="CSV Export"/>
            </p>
        </div>
    </li>
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